Identification and analysis of functional elements in 1% of the
human genome by the ENCODE project

The ENCODE consortium

Nature. 447:779-816, 2007.

Abstract

We report the generation and analysis of functional data from
multiple, diverse experiments performed on a targeted 1% of the human
genome as part of the pilot phase of the ENCODE Project. These data
have been further integrated and augmented by a number of evolutionary
and computational analyses. Together, our results advance the
collective knowledge about human genome function in several major
areas. First, our studies provide convincing evidence that the genome
is pervasively transcribed, such that the majority of its bases can be
found in primary transcripts, including non-protein-coding
transcripts, and those that extensively overlap one another. Second,
systematic examination of transcriptional regulation has yielded new
understanding about transcription start sites, including their
relationship to specific regulatory sequences and features of
chromatin accessibility and histone modification. Third, a more
sophisticated view of chromatin structure has emerged, including its
inter-relationship with DNA replication and transcriptional
regulation. Finally, integration of these new sources of information,
in particular with respect to mammalian evolution based on inter- and
intra-species sequence comparisons, has yielded new mechanistic and
evolutionary insights concerning the functional landscape of the human
genome. Together, these studies are defining a path for pursuit of a
more comprehensive characterization of human genome function.